tines 0.0.277 → 0.0.279

package/dist/index.js

@@ -3436,6 +3436,7 @@ var PROMPT_MAX_BYTES = 32 * 1024;
 var SKILL_MAX_FILES = 20;
 var SKILL_MAX_TOTAL_BYTES = 100 * 1024;
 var ENV_VALUE_MAX_BYTES = 16 * 1024;
+var SKILL_NAME_PATTERN = /^[a-z0-9-]+$/;
 var AGENT_GUIDELINES_NAME = "agent-guidelines";
 var JOURNAL_NAME = "journal";
 var AGENT_GUIDELINES_BODY = `You are an agent working on a Tines issue over its HTTP API / CLI. Beyond doing the work, leave the workspace smarter than you found it. Four places to write, chosen by who should inherit what you learned:
@@ -3604,8 +3605,8 @@ function str(v) {
 function isoTime(v) {
   return typeof v === "number" && Number.isFinite(v) ? new Date(v).toISOString() : "an unknown time";
 }
-function joinChanged(v, sep4) {
-  return Array.isArray(v) ? v.join(sep4) : "";
+function joinChanged(v, sep5) {
+  return Array.isArray(v) ? v.join(sep5) : "";
 }
 function action(type) {
   return type.split(".")[1] ?? type;
@@ -5946,11 +5947,11 @@ function assertNewStatesHavePrompts(states, prompts) {
   }
 }
 function parseScheduleRef(ref) {
-  const sep4 = ref.indexOf("/");
-  if (sep4 < 1 || sep4 === ref.length - 1) {
+  const sep5 = ref.indexOf("/");
+  if (sep5 < 1 || sep5 === ref.length - 1) {
     throw new CliError(`schedule reference must look like <project>/<name>, got "${ref}"`);
   }
-  return { project: ref.slice(0, sep4), name: ref.slice(sep4 + 1) };
+  return { project: ref.slice(0, sep5), name: ref.slice(sep5 + 1) };
 }
 function parseIssueRef(ref) {
   const match = ref.match(/^(.+)\/(\d+)$/);
@@ -5958,12 +5959,12 @@ function parseIssueRef(ref) {
   return { project: match[1], number: Number.parseInt(match[2], 10) };
 }
 function parseFileSpec(spec) {
-  const sep4 = spec.indexOf("=");
-  if (sep4 < 1 || sep4 === spec.length - 1) {
+  const sep5 = spec.indexOf("=");
+  if (sep5 < 1 || sep5 === spec.length - 1) {
     throw new CliError(`--file must look like <path>=@<local-file>, got "${spec}"`);
   }
-  const path2 = spec.slice(0, sep4);
-  const source = spec.slice(sep4 + 1);
+  const path2 = spec.slice(0, sep5);
+  const source = spec.slice(sep5 + 1);
   if (!source.startsWith("@")) {
     throw new CliError(
       `skill file content always comes from a local file: --file ${path2}=@<local-file>`
@@ -5977,10 +5978,10 @@ function parseFileSpec(spec) {
   }
 }
 function parseTargetSpec(spec) {
-  const sep4 = spec.lastIndexOf(":");
-  if (sep4 === -1) return { name: spec };
-  const name2 = spec.slice(0, sep4);
-  const tier = spec.slice(sep4 + 1);
+  const sep5 = spec.lastIndexOf(":");
+  if (sep5 === -1) return { name: spec };
+  const name2 = spec.slice(0, sep5);
+  const tier = spec.slice(sep5 + 1);
   if (!name2) throw new CliError(`target must look like <runner>[:tier], got "${spec}"`);
   if (!MODEL_TIERS.includes(tier)) {
     throw new CliError(`unknown tier "${tier}" in "${spec}" (tiers: ${MODEL_TIERS.join(", ")})`);
@@ -6224,12 +6225,12 @@ async function resolveLabelFlag(api, ref) {
   return match.id;
 }
 async function resolveStateFlag(api, ref) {
-  const sep4 = ref.indexOf("/");
-  if (sep4 < 1 || sep4 === ref.length - 1) {
+  const sep5 = ref.indexOf("/");
+  if (sep5 < 1 || sep5 === ref.length - 1) {
     die(`--state must look like <workflow>/<state>, got "${ref}"`);
   }
-  const workflow2 = await resolveWorkflow(api, ref.slice(0, sep4));
-  const stateRef2 = ref.slice(sep4 + 1);
+  const workflow2 = await resolveWorkflow(api, ref.slice(0, sep5));
+  const stateRef2 = ref.slice(sep5 + 1);
   const state = workflow2.states.find((s) => s.name === stateRef2) ?? workflow2.states.find((s) => s.id === stateRef2);
   if (!state) {
     die(
@@ -6281,7 +6282,7 @@ type: ${item.artifact_type ?? "artifact"}`);
 ${item.body}`);
   } else if (item.kind === "skill") {
     console.log(`
-files (seeded at skills/${item.name}/):`);
+files (seeded at .agents/skills/${item.name}/):`);
     for (const f of item.files ?? []) {
       console.log(`  ${f.path}  (${Buffer.byteLength(f.content, "utf8")} bytes)`);
     }
@@ -6510,8 +6511,8 @@ function register(program3) {
 }
 
 // src/commands/issues.ts
-import { existsSync as existsSync3, mkdirSync as mkdirSync2, readdirSync, readFileSync as readFileSync5, statSync as statSync2, writeFileSync as writeFileSync2 } from "node:fs";
-import { basename, dirname as dirname2, join as join2 } from "node:path";
+import { existsSync as existsSync4, mkdirSync as mkdirSync3, readdirSync, readFileSync as readFileSync5, statSync as statSync2, writeFileSync as writeFileSync3 } from "node:fs";
+import { basename, dirname as dirname2, join as join3 } from "node:path";
 import { createInterface } from "node:readline/promises";
 
 // src/issue-transfer.ts
@@ -7142,6 +7143,97 @@ function buildRecurrence(opts) {
   }
 }
 
+// src/skills.ts
+import { randomUUID } from "node:crypto";
+import { existsSync as existsSync3, lstatSync, mkdirSync as mkdirSync2, renameSync as renameSync2, rmSync as rmSync2, writeFileSync as writeFileSync2 } from "node:fs";
+import { isAbsolute, join as join2, relative, resolve, sep } from "node:path";
+var SKILLS_DIRECTORY = ".agents/skills";
+function validateRelativePath(value, label) {
+  if (!value || isAbsolute(value) || value.startsWith("/") || value.includes("\\")) {
+    throw new Error(`${label} must be a relative path using forward slashes (got "${value}")`);
+  }
+  if (value.includes("=")) throw new Error(`${label} cannot contain "=" (got "${value}")`);
+  const segments = value.split("/");
+  if (segments.some((segment) => !segment || segment === "." || segment === "..")) {
+    throw new Error(`${label} cannot contain empty, ".", or ".." segments (got "${value}")`);
+  }
+  return segments;
+}
+function isPrefix(left, right) {
+  return left.length <= right.length && left.every((segment, index) => segment.toLowerCase() === right[index]?.toLowerCase());
+}
+function assertNoSkillRepoOverlap(repoDirs) {
+  const skills = SKILLS_DIRECTORY.split("/");
+  for (const dir of repoDirs) {
+    const repo = validateRelativePath(dir, "Repository checkout directory");
+    if (isPrefix(repo, skills) || isPrefix(skills, repo)) {
+      throw new Error(
+        `Repository checkout directory "${dir}" overlaps generated skill directory "${SKILLS_DIRECTORY}"`
+      );
+    }
+  }
+}
+function rejectSymlink(path2, label) {
+  if (!existsSync3(path2)) return;
+  const stat2 = lstatSync(path2);
+  if (stat2.isSymbolicLink()) throw new Error(`${label} must not be a symlink: ${path2}`);
+  if (!stat2.isDirectory()) throw new Error(`${label} must be a directory: ${path2}`);
+}
+function materializeSkills(root, skills) {
+  const seenSkills = /* @__PURE__ */ new Set();
+  for (const skill of skills) {
+    if (!SKILL_NAME_PATTERN.test(skill.name)) {
+      throw new Error(`Invalid skill name "${skill.name}"; expected [a-z0-9-]+`);
+    }
+    if (seenSkills.has(skill.name)) throw new Error(`Duplicate skill name "${skill.name}"`);
+    seenSkills.add(skill.name);
+    const seenFiles = /* @__PURE__ */ new Set();
+    for (const file of skill.files) {
+      validateRelativePath(file.path, `Skill "${skill.name}" file path`);
+      if (seenFiles.has(file.path)) {
+        throw new Error(`Skill "${skill.name}" file path "${file.path}" is duplicated`);
+      }
+      seenFiles.add(file.path);
+    }
+  }
+  const agentsDir = join2(root, ".agents");
+  const destination = join2(agentsDir, "skills");
+  rejectSymlink(agentsDir, "Agent metadata directory");
+  rejectSymlink(destination, "Generated skill directory");
+  mkdirSync2(agentsDir, { recursive: true });
+  const suffix = randomUUID();
+  const staged = join2(agentsDir, `.skills-stage-${suffix}`);
+  const backup = join2(agentsDir, `.skills-backup-${suffix}`);
+  try {
+    mkdirSync2(staged);
+    for (const skill of skills) {
+      const skillDir = join2(staged, skill.name);
+      mkdirSync2(skillDir, { recursive: true });
+      for (const file of skill.files) {
+        const target = resolve(skillDir, ...file.path.split("/"));
+        const within = relative(skillDir, target);
+        if (within === ".." || within.startsWith(`..${sep}`) || isAbsolute(within)) {
+          throw new Error(`Skill "${skill.name}" file escapes its directory: ${file.path}`);
+        }
+        mkdirSync2(resolve(target, ".."), { recursive: true });
+        writeFileSync2(target, file.content);
+      }
+    }
+    if (existsSync3(destination)) renameSync2(destination, backup);
+    try {
+      renameSync2(staged, destination);
+    } catch (error) {
+      if (existsSync3(backup) && !existsSync3(destination)) renameSync2(backup, destination);
+      throw error;
+    }
+    rmSync2(backup, { recursive: true, force: true });
+  } finally {
+    rmSync2(staged, { recursive: true, force: true });
+    if (existsSync3(backup) && !existsSync3(destination)) renameSync2(backup, destination);
+    else rmSync2(backup, { recursive: true, force: true });
+  }
+}
+
 // src/commands/issues.ts
 var systemTimezone = () => Intl.DateTimeFormat().resolvedOptions().timeZone;
 function printIssueLinks(links) {
@@ -7233,7 +7325,7 @@ function walkFolder(dir) {
   const files2 = [];
   const walk = (abs, rel) => {
     for (const entry of readdirSync(abs, { withFileTypes: true })) {
-      const nextAbs = join2(abs, entry.name);
+      const nextAbs = join3(abs, entry.name);
       const nextRel = rel ? `${rel}/${entry.name}` : entry.name;
       if (entry.isDirectory()) walk(nextAbs, nextRel);
       else if (entry.isFile()) {
@@ -7693,7 +7785,7 @@ function register2(program3) {
       "Print an issue's effective context (the assembled bundle for its current state)"
     ).option(
       "--out <dir>",
-      "write the bundle to a directory: prompt.md, skills/<name>/\u2026, repos.json"
+      "write the bundle to a directory: prompt.md, .agents/skills/<name>/\u2026, repos.json"
     ).option("--force", "allow --out into a non-empty directory")
   ).action(async (ref, opts) => {
     const api = client(opts);
@@ -7731,23 +7823,18 @@ skills: ${context2.skills.map((s) => s.name).join(", ")}`);
         `refusing to write: checkout-directory conflict${context2.conflicts.length === 1 ? "" : "s"} among the effective repos (${context2.conflicts.map((c) => `"${c.dir}": ${c.item_ids.join(", ")}`).join("; ")}); rename or re-dir the items first`
       );
     }
-    if (existsSync3(opts.out) && readdirSync(opts.out).length > 0 && !opts.force) {
+    if (existsSync4(opts.out) && readdirSync(opts.out).length > 0 && !opts.force) {
       die(`refusing to write into non-empty directory ${opts.out} (pass --force to override)`);
     }
-    mkdirSync2(opts.out, { recursive: true });
-    writeFileSync2(
-      join2(opts.out, "prompt.md"),
+    assertNoSkillRepoOverlap(context2.repos.map((repo) => repo.dir));
+    mkdirSync3(opts.out, { recursive: true });
+    materializeSkills(opts.out, context2.skills);
+    writeFileSync3(
+      join3(opts.out, "prompt.md"),
       context2.prompt.text ? `${context2.prompt.text}
 ` : ""
     );
-    for (const skill of context2.skills) {
-      for (const file of skill.files) {
-        const target = join2(opts.out, "skills", skill.name, file.path);
-        mkdirSync2(dirname2(target), { recursive: true });
-        writeFileSync2(target, file.content);
-      }
-    }
-    writeFileSync2(join2(opts.out, "repos.json"), `${JSON.stringify(context2.repos, null, 2)}
+    writeFileSync3(join3(opts.out, "repos.json"), `${JSON.stringify(context2.repos, null, 2)}
 `);
     console.log(
       `wrote ${opts.out}/prompt.md, ${context2.skills.length} skill${context2.skills.length === 1 ? "" : "s"}, repos.json (${context2.repos.length} repo${context2.repos.length === 1 ? "" : "s"})`
@@ -8018,10 +8105,10 @@ files (v${artifact.current_version.version}):`);
         if (opts.out === void 0) {
           die(`artifact "${name2}" is a folder \u2014 pass --out <dir> to write its tree`);
         }
-        if (existsSync3(opts.out) && !statSync2(opts.out).isDirectory()) {
+        if (existsSync4(opts.out) && !statSync2(opts.out).isDirectory()) {
           die(`--out for a folder must be a directory, and "${opts.out}" is a file`);
         }
-        if (existsSync3(opts.out) && readdirSync(opts.out).length > 0) {
+        if (existsSync4(opts.out) && readdirSync(opts.out).length > 0) {
           die(
             `refusing to write folder artifact into non-empty directory "${opts.out}"; choose a new or empty directory`
           );
@@ -8033,9 +8120,9 @@ files (v${artifact.current_version.version}):`);
             version: opts.version,
             path: file.path
           });
-          const target2 = join2(opts.out, file.path);
-          mkdirSync2(dirname2(target2), { recursive: true });
-          writeFileSync2(target2, Buffer.from(content2.bytes));
+          const target2 = join3(opts.out, file.path);
+          mkdirSync3(dirname2(target2), { recursive: true });
+          writeFileSync3(target2, Buffer.from(content2.bytes));
           total += content2.bytes.byteLength;
         }
         return console.log(
@@ -8046,10 +8133,10 @@ files (v${artifact.current_version.version}):`);
       const bytes2 = Buffer.from(content.bytes);
       if (opts.out !== void 0) {
         let target2 = opts.out;
-        if (existsSync3(target2) && statSync2(target2).isDirectory()) {
-          target2 = join2(target2, version.filename ?? name2);
+        if (existsSync4(target2) && statSync2(target2).isDirectory()) {
+          target2 = join3(target2, version.filename ?? name2);
         }
-        writeFileSync2(target2, bytes2);
+        writeFileSync3(target2, bytes2);
         return console.log(`wrote ${target2} (${bytes2.byteLength} bytes, ${content.content_type})`);
       }
       if ((content.content_type ?? "").startsWith("text/")) {
@@ -8057,7 +8144,7 @@ files (v${artifact.current_version.version}):`);
         return;
       }
       const target = version.filename ?? name2;
-      writeFileSync2(target, bytes2);
+      writeFileSync3(target, bytes2);
       console.log(`wrote ${target} (${bytes2.byteLength} bytes, ${content.content_type})`);
     }
   );
@@ -8794,17 +8881,17 @@ function register7(program3) {
 import { spawn as spawn3 } from "node:child_process";
 import {
   createWriteStream,
-  existsSync as existsSync5,
-  mkdirSync as mkdirSync4,
+  existsSync as existsSync6,
+  mkdirSync as mkdirSync5,
   readFileSync as readFileSync10,
   realpathSync,
-  rmSync as rmSync3,
+  rmSync as rmSync4,
   statSync as statSync4,
   unlinkSync as unlinkSync2,
-  writeFileSync as writeFileSync3
+  writeFileSync as writeFileSync4
 } from "node:fs";
-import { randomUUID } from "node:crypto";
-import { dirname as dirname4, join as join6 } from "node:path";
+import { randomUUID as randomUUID2 } from "node:crypto";
+import { dirname as dirname4, join as join7 } from "node:path";
 import { StringDecoder as StringDecoder2 } from "node:string_decoder";
 
 // src/version.ts
@@ -9175,7 +9262,7 @@ var CodexStreamRenderer = class {
 
 // src/daemon/codex-rollout.ts
 import { open, opendir, realpath, stat } from "node:fs/promises";
-import { isAbsolute, join as join3, relative, resolve, sep } from "node:path";
+import { isAbsolute as isAbsolute2, join as join4, relative as relative2, resolve as resolve2, sep as sep2 } from "node:path";
 import { homedir as homedir2 } from "node:os";
 import { StringDecoder } from "node:string_decoder";
 var CODEX_ROLLOUT_MAX_BYTES = 128 * 1024 * 1024;
@@ -9301,7 +9388,7 @@ function reconcileCodexRollout(records, input2) {
 }
 function resolveCodexHome(env, workspace) {
   const configured = env.CODEX_HOME;
-  return configured ? resolve(workspace, configured) : join3(homedir2(), ".codex");
+  return configured ? resolve2(workspace, configured) : join4(homedir2(), ".codex");
 }
 function dateDirectories(startedAt, endedAt) {
   const first = new Date(startedAt);
@@ -9313,7 +9400,7 @@ function dateDirectories(startedAt, endedAt) {
   const result = [];
   for (let date = first; date <= last; date = new Date(date.getTime() + 864e5)) {
     result.push(
-      join3(
+      join4(
         String(date.getUTCFullYear()),
         String(date.getUTCMonth() + 1).padStart(2, "0"),
         String(date.getUTCDate()).padStart(2, "0")
@@ -9380,7 +9467,7 @@ async function collectCodexRequestContext(input2) {
     return unavailable("thread_id_missing");
   const dates = dateDirectories(input2.startedAt, input2.endedAt);
   if (!dates) return unavailable("limit_exceeded");
-  const sessions = join3(input2.codexHome, "sessions");
+  const sessions = join4(input2.codexHome, "sessions");
   let root;
   try {
     root = await realpath(sessions);
@@ -9392,7 +9479,7 @@ async function collectCodexRequestContext(input2) {
   const deadline = Date.now() + CODEX_ROLLOUT_TIMEOUT_MS;
   try {
     for (const date of dates) {
-      const directory = join3(root, date);
+      const directory = join4(root, date);
       let stream;
       try {
         stream = await opendir(directory);
@@ -9402,14 +9489,14 @@ async function collectCodexRequestContext(input2) {
       for await (const entry of stream) {
         if (++entries > 2e4 || Date.now() > deadline) return unavailable("limit_exceeded");
         if ((entry.isFile() || entry.isSymbolicLink()) && entry.name.startsWith("rollout-") && entry.name.endsWith(`-${input2.threadId}.jsonl`))
-          candidates.push(join3(directory, entry.name));
+          candidates.push(join4(directory, entry.name));
       }
     }
     if (candidates.length === 0) return unavailable("rollout_missing");
     if (candidates.length !== 1) return unavailable("rollout_ambiguous");
     const candidate = await realpath(candidates[0]);
-    const inside = relative(root, candidate);
-    if (inside.startsWith(`..${sep}`) || inside === ".." || isAbsolute(inside))
+    const inside = relative2(root, candidate);
+    if (inside.startsWith(`..${sep2}`) || inside === ".." || isAbsolute2(inside))
       return unavailable("unsafe_path");
     const before = await stat(candidate);
     if (!before.isFile() || before.size > CODEX_ROLLOUT_MAX_BYTES)
@@ -9530,11 +9617,11 @@ var DURATION = /(\d+)\s*([dhms])/g;
 function parseResetTime(text4, now) {
   const raw = text4.trim();
   if (!raw) return null;
-  const relative2 = raw.match(/^in\s+(.+)$/i);
-  if (relative2) {
+  const relative3 = raw.match(/^in\s+(.+)$/i);
+  if (relative3) {
     let ms = 0;
     let matched = false;
-    for (const [, amount, unit] of relative2[1].matchAll(DURATION)) {
+    for (const [, amount, unit] of relative3[1].matchAll(DURATION)) {
       const n = Number(amount);
       ms += n * { d: 864e5, h: 36e5, m: 6e4, s: 1e3 }[unit];
       matched = true;
@@ -9658,12 +9745,12 @@ function failure(harness, daemonVersion, reason) {
   };
 }
 function run(file, args) {
-  return new Promise((resolve2, reject) => {
+  return new Promise((resolve3, reject) => {
     execFile(
       file,
       args,
       { timeout: DEADLINE_MS, maxBuffer: MAX_STDOUT },
-      (error, stdout) => error ? reject(error) : resolve2(stdout)
+      (error, stdout) => error ? reject(error) : resolve3(stdout)
     );
   });
 }
@@ -9716,7 +9803,7 @@ async function discoverCodex(daemonVersion) {
   } catch (error) {
     return failure("codex", daemonVersion, error instanceof Error ? error.message : String(error));
   }
-  return new Promise((resolve2) => {
+  return new Promise((resolve3) => {
     const child = spawn("codex", ["app-server"], { stdio: ["pipe", "pipe", "ignore"] });
     let buffer = "";
     let bytes2 = 0;
@@ -9728,7 +9815,7 @@ async function discoverCodex(daemonVersion) {
       settled = true;
       clearTimeout(timer);
       child.kill();
-      resolve2(report);
+      resolve3(report);
     };
     const fail = (reason) => finish(failure("codex", daemonVersion, reason));
     const sendList = (cursor) => {
@@ -9826,11 +9913,11 @@ var EffortCapabilityRefresher = class {
 
 // src/daemon/cli-refresh.ts
 import { spawn as spawn2 } from "node:child_process";
-import { existsSync as existsSync4, mkdirSync as mkdirSync3, readFileSync as readFileSync8 } from "node:fs";
-import { dirname as dirname3, join as join4 } from "node:path";
+import { existsSync as existsSync5, mkdirSync as mkdirSync4, readFileSync as readFileSync8 } from "node:fs";
+import { dirname as dirname3, join as join5 } from "node:path";
 
 // src/daemon/support.ts
-import { delimiter, sep as sep2 } from "node:path";
+import { delimiter, sep as sep3 } from "node:path";
 var HARNESS_KINDS = ["claude_code", "codex", "custom"];
 var KEEP_WORKSPACES_MODES = ["never", "failed", "always"];
 function keepWorkspace(mode, outcome) {
@@ -10144,7 +10231,7 @@ function pendingSelfUpdate(cli, running) {
   return isNewerVersion(cli.version, running) ? cli.version : null;
 }
 function pathWithin(path2, dir) {
-  const root = dir.endsWith(sep2) ? dir : dir + sep2;
+  const root = dir.endsWith(sep3) ? dir : dir + sep3;
   return path2.startsWith(root);
 }
 function buildSpawnEnv(base, opts) {
@@ -10217,14 +10304,14 @@ var SecretRedactor = class {
 var PACKAGE = "tines";
 var NPM_ARGS = ["--min-release-age=0", "--no-audit", "--no-fund", "--loglevel=error"];
 function agentCliPrefix(configDir) {
-  return join4(configDir, "cli");
+  return join5(configDir, "cli");
 }
 function binDirOf(prefix) {
-  return join4(prefix, "node_modules", ".bin");
+  return join5(prefix, "node_modules", ".bin");
 }
 function installedVersion(prefix) {
   try {
-    const pkg = readFileSync8(join4(prefix, "node_modules", PACKAGE, "package.json"), "utf8");
+    const pkg = readFileSync8(join5(prefix, "node_modules", PACKAGE, "package.json"), "utf8");
     const version = JSON.parse(pkg).version;
     return typeof version === "string" ? version : null;
   } catch {
@@ -10233,11 +10320,11 @@ function installedVersion(prefix) {
 }
 function lastGood(prefix) {
   const binDir = binDirOf(prefix);
-  if (!existsSync4(join4(binDir, PACKAGE))) return AMBIENT_CLI;
+  if (!existsSync5(join5(binDir, PACKAGE))) return AMBIENT_CLI;
   return { binDir, version: installedVersion(prefix), source: "stale" };
 }
 function runNpm(file, args, cwd, timeoutMs) {
-  return new Promise((resolve2) => {
+  return new Promise((resolve3) => {
     let output = "";
     let done = false;
     let timedOut = false;
@@ -10252,7 +10339,7 @@ function runNpm(file, args, cwd, timeoutMs) {
       if (done) return;
       done = true;
       clearTimeout(timer);
-      resolve2({ ...result, timedOut, output });
+      resolve3({ ...result, timedOut, output });
     };
     child.stdout?.on("data", (data) => output += data.toString("utf8"));
     child.stderr?.on("data", (data) => output += data.toString("utf8"));
@@ -10270,7 +10357,7 @@ async function installAgentCli(opts) {
   const prefix = agentCliPrefix(opts.configDir);
   const timeoutMs = opts.timeoutMs ?? 6e4;
   try {
-    mkdirSync3(prefix, { recursive: true });
+    mkdirSync4(prefix, { recursive: true });
   } catch (err) {
     opts.log(`agent CLI refresh: cannot create ${prefix} (${message(err)})`);
     return AMBIENT_CLI;
@@ -10278,8 +10365,8 @@ async function installAgentCli(opts) {
   const args = ["install", "--prefix", prefix, `${PACKAGE}@latest`, ...NPM_ARGS];
   let result = await runNpm("npm", args, prefix, timeoutMs);
   if (result.spawnError?.code === "ENOENT") {
-    const sibling = join4(dirname3(process.execPath), "npm");
-    if (existsSync4(sibling)) result = await runNpm(sibling, args, prefix, timeoutMs);
+    const sibling = join5(dirname3(process.execPath), "npm");
+    if (existsSync5(sibling)) result = await runNpm(sibling, args, prefix, timeoutMs);
   }
   if (result.code !== 0) {
     const fallback = lastGood(prefix);
@@ -10304,13 +10391,13 @@ function message(err) {
 import { arch, hostname, platform } from "node:os";
 
 // src/daemon/store.ts
-import { readdirSync as readdirSync2, readFileSync as readFileSync9, rmSync as rmSync2, statSync as statSync3 } from "node:fs";
-import { join as join5 } from "node:path";
+import { readdirSync as readdirSync2, readFileSync as readFileSync9, rmSync as rmSync3, statSync as statSync3 } from "node:fs";
+import { join as join6 } from "node:path";
 function credentialsKey(url, name2) {
   return `${url.replace(/\/+$/, "")}#${name2}`;
 }
 function credentialsPath(dir) {
-  return join5(dir, "runners.json");
+  return join6(dir, "runners.json");
 }
 function loadRunnerCredentials(dir, url, name2) {
   const all = readJsonFile(credentialsPath(dir));
@@ -10333,7 +10420,7 @@ function clearRunnerCredentials(dir, url, name2) {
   writeJsonFile(path2, all, { secret: true });
 }
 function daemonStatePath(dir, runnerId) {
-  return join5(dir, `daemon-state-${runnerId}.json`);
+  return join6(dir, `daemon-state-${runnerId}.json`);
 }
 function loadDaemonState(path2) {
   const state = readJsonFile(path2);
@@ -10346,7 +10433,7 @@ function saveDaemonState(path2, runs) {
   writeJsonFile(path2, { runs });
 }
 function daemonDeclinesPath(dir, runnerId) {
-  return join5(dir, `daemon-declines-${runnerId}.json`);
+  return join6(dir, `daemon-declines-${runnerId}.json`);
 }
 function loadDaemonDeclines(path2) {
   const state = readJsonFile(path2);
@@ -10376,10 +10463,10 @@ function processStartTimeMs(pid) {
   }
 }
 function workspacesDir(configDir) {
-  return join5(configDir, "workspaces");
+  return join6(configDir, "workspaces");
 }
 function keptMarkerPath(workspace) {
-  return join5(workspace, "kept.json");
+  return join6(workspace, "kept.json");
 }
 function writeKeptMarker(workspace, marker) {
   writeJsonFile(keptMarkerPath(workspace), marker);
@@ -10401,7 +10488,7 @@ function listKeptWorkspaces(configDir) {
   }
   const kept = [];
   for (const name2 of names) {
-    const path2 = join5(root, name2);
+    const path2 = join6(root, name2);
     const marker = readKeptMarker(path2);
     if (marker) kept.push({ ...marker, path: path2 });
   }
@@ -10422,7 +10509,7 @@ function pruneKeptWorkspaces(configDir, opts) {
   const removed = [];
   for (const entry of doomed) {
     try {
-      rmSync2(entry.path, { recursive: true, force: true });
+      rmSync3(entry.path, { recursive: true, force: true });
       removed.push(entry);
     } catch {
     }
@@ -10438,7 +10525,7 @@ function directorySizeBytes(path2) {
     return 0;
   }
   for (const entry of entries) {
-    const child = join5(path2, entry.name);
+    const child = join6(path2, entry.name);
     if (entry.isDirectory()) total += directorySizeBytes(child);
     else if (entry.isFile()) {
       try {
@@ -10491,7 +10578,7 @@ async function uploadRawLog(run3) {
   if (!path2 || !run3.rawUpload) return;
   run3.rawSpoolPath = void 0;
   try {
-    await new Promise((resolve2) => run3.rawSpool?.end(resolve2) ?? resolve2());
+    await new Promise((resolve3) => run3.rawSpool?.end(resolve3) ?? resolve3());
     const size = statSync4(path2).size;
     if (size > 0) {
       let body = readFileSync10(path2);
@@ -10516,7 +10603,7 @@ async function uploadRawLog(run3) {
   }
 }
 var log = (message3) => console.log(`[${(/* @__PURE__ */ new Date()).toISOString().slice(11, 19)}] ${message3}`);
-var sleep = (ms) => new Promise((resolve2) => setTimeout(resolve2, ms));
+var sleep = (ms) => new Promise((resolve3) => setTimeout(resolve3, ms));
 function killTree(pid, signal) {
   try {
     process.kill(-pid, signal);
@@ -10536,10 +10623,10 @@ function pidAlive(pid) {
   }
 }
 async function runDaemon(opts) {
-  const instanceId = randomUUID();
+  const instanceId = randomUUID2();
   const baseUrl = opts.url.replace(/\/+$/, "");
-  mkdirSync4(opts.configDir, { recursive: true });
-  mkdirSync4(workspacesDir(opts.configDir), { recursive: true, mode: 448 });
+  mkdirSync5(opts.configDir, { recursive: true });
+  mkdirSync5(workspacesDir(opts.configDir), { recursive: true, mode: 448 });
   const sweepKeptWorkspaces = () => {
     const removed = pruneKeptWorkspaces(opts.configDir, {
       maxAgeMs: opts.keepWorkspacesForHours * 36e5,
@@ -10554,10 +10641,10 @@ async function runDaemon(opts) {
   sweepKeptWorkspaces();
   const settleWorkspace = (workspace, keep, marker) => {
     if (!keep) {
-      rmSync3(workspace, { recursive: true, force: true });
+      rmSync4(workspace, { recursive: true, force: true });
       return;
     }
-    if (!existsSync5(workspace)) return;
+    if (!existsSync6(workspace)) return;
     try {
       writeKeptMarker(workspace, { ...marker, kept_at: (/* @__PURE__ */ new Date()).toISOString() });
       log(`run ${marker.run_id}: workspace kept at ${workspace}`);
@@ -10602,7 +10689,7 @@ async function runDaemon(opts) {
   const selfUpdate = opts.selfUpdate && opts.cliRefresh && managedInstall;
   if (opts.selfUpdate && opts.cliRefresh) {
     log(
-      managedInstall ? `self-update: on \u2014 this daemon (tines ${DAEMON_VERSION}) runs from ${prefix} and will restart once idle after a newer release is installed there` : `self-update: off \u2014 this daemon (tines ${DAEMON_VERSION}) runs from ${selfPath ?? process.argv[1] ?? "?"}, not ${prefix}; launch it from ${join6(prefix, "node_modules", ".bin", "tines")} to have refreshes apply on restart \u2014 \`tines runner install --name ${opts.name} --harness ${opts.harness.replaceAll("_", "-")}\` sets that up as a service (docs/runner-daemon.md)`
+      managedInstall ? `self-update: on \u2014 this daemon (tines ${DAEMON_VERSION}) runs from ${prefix} and will restart once idle after a newer release is installed there` : `self-update: off \u2014 this daemon (tines ${DAEMON_VERSION}) runs from ${selfPath ?? process.argv[1] ?? "?"}, not ${prefix}; launch it from ${join7(prefix, "node_modules", ".bin", "tines")} to have refreshes apply on restart \u2014 \`tines runner install --name ${opts.name} --harness ${opts.harness.replaceAll("_", "-")}\` sets that up as a service (docs/runner-daemon.md)`
     );
   }
   let pendingUpdate = null;
@@ -10765,13 +10852,13 @@ async function runDaemon(opts) {
     const secretEnvValues = (assignment.env ?? []).filter((e) => e.secret).map((e) => e.value);
     const runId = assignment.run.id;
     if (table2.has(runId)) return;
-    const resume = assignment.resume && existsSync5(assignment.resume.workspace_path) ? assignment.resume : null;
+    const resume = assignment.resume && existsSync6(assignment.resume.workspace_path) ? assignment.resume : null;
     if (assignment.resume && !resume) {
       log(
         `run ${runId}: resume workspace ${assignment.resume.workspace_path} is gone; launching fresh`
       );
     }
-    const workspace = resume ? resume.workspace_path : join6(workspacesDir(opts.configDir), runId);
+    const workspace = resume ? resume.workspace_path : join7(workspacesDir(opts.configDir), runId);
     const issueLabel = assignment.run.issue_ref ? `${assignment.run.issue_ref.project_name}/${assignment.run.issue_ref.number}` : void 0;
     const run3 = {
       runId,
@@ -10813,25 +10900,40 @@ async function runDaemon(opts) {
       resume ? `run ${runId} assigned (issue ${issueLabel ?? assignment.run.issue_id}); resuming run ${resume.previous_run_id} in ${workspace}` : `run ${runId} assigned (issue ${issueLabel ?? assignment.run.issue_id}); materializing workspace`
     );
     try {
+      const currentRepoDirs = assignment.bundle.repos.map((repo) => repo.dir);
+      let retainedRepoDirs = [];
+      if (resume) {
+        const retainedPath = join7(workspace, "repos.json");
+        let retained;
+        try {
+          retained = JSON.parse(readFileSync10(retainedPath, "utf8"));
+        } catch (error) {
+          throw new Error(
+            `cannot safely refresh skills: retained ${retainedPath} is unreadable or invalid JSON (${message2(error)})`
+          );
+        }
+        if (!Array.isArray(retained) || retained.some(
+          (repo) => !repo || typeof repo !== "object" || typeof repo.dir !== "string"
+        )) {
+          throw new Error(
+            `cannot safely refresh skills: retained ${retainedPath} must be an array of repositories with string dir fields`
+          );
+        }
+        retainedRepoDirs = retained.map((repo) => repo.dir);
+      }
+      assertNoSkillRepoOverlap([...currentRepoDirs, ...retainedRepoDirs]);
       if (!resume) {
-        rmSync3(workspace, { recursive: true, force: true });
-        mkdirSync4(workspace, { recursive: true });
+        rmSync4(workspace, { recursive: true, force: true });
+        mkdirSync5(workspace, { recursive: true });
       } else {
-        rmSync3(join6(workspace, "kept.json"), { force: true });
+        rmSync4(join7(workspace, "kept.json"), { force: true });
       }
-      writeFileSync3(join6(workspace, "prompt.md"), `${assignment.prompt}
+      materializeSkills(workspace, assignment.bundle.skills);
+      writeFileSync4(join7(workspace, "prompt.md"), `${assignment.prompt}
 `);
       if (!resume)
-        for (const skill of assignment.bundle.skills) {
-          for (const file of skill.files) {
-            const target = join6(workspace, "skills", skill.name, file.path);
-            mkdirSync4(dirname4(target), { recursive: true });
-            writeFileSync3(target, file.content);
-          }
-        }
-      if (!resume)
-        writeFileSync3(
-          join6(workspace, "repos.json"),
+        writeFileSync4(
+          join7(workspace, "repos.json"),
           `${JSON.stringify(assignment.bundle.repos, null, 2)}
 `
         );
@@ -10865,7 +10967,7 @@ async function runDaemon(opts) {
       );
       const harnessInput = {
         workspace,
-        promptFile: join6(workspace, "prompt.md"),
+        promptFile: join7(workspace, "prompt.md"),
         prompt: assignment.prompt,
         model: assignment.run.model,
         effort: assignment.effort?.value ?? null,
@@ -10931,8 +11033,8 @@ async function runDaemon(opts) {
           (event) => limiter.noteStreamEvent(event)
         );
         run3.renderer = renderer;
-        const spoolPath = join6(opts.configDir, "rawlogs", `${runId}.ndjson`);
-        mkdirSync4(dirname4(spoolPath), { recursive: true });
+        const spoolPath = join7(opts.configDir, "rawlogs", `${runId}.ndjson`);
+        mkdirSync5(dirname4(spoolPath), { recursive: true });
         run3.rawSpoolPath = spoolPath;
         run3.rawSpool = createWriteStream(spoolPath);
         run3.rawUpload = (body) => client2.putRunLogRaw(runId, body);
@@ -11185,12 +11287,12 @@ function realpathOrNull(path2) {
   }
 }
 function runGit(args, cwd, batcher) {
-  return new Promise((resolve2) => {
+  return new Promise((resolve3) => {
     const child = spawn3("git", args, { cwd, stdio: ["ignore", "pipe", "pipe"] });
     child.stdout?.on("data", (data) => batcher.append(data.toString("utf8")));
     child.stderr?.on("data", (data) => batcher.append(data.toString("utf8")));
-    child.on("error", () => resolve2(127));
-    child.on("exit", (code) => resolve2(code ?? 1));
+    child.on("error", () => resolve3(127));
+    child.on("exit", (code) => resolve3(code ?? 1));
   });
 }
 
@@ -11274,14 +11376,14 @@ function harnessFlag(harness) {
 
 // src/commands/runner-service.ts
 import { execFile as execFile2 } from "node:child_process";
-import { existsSync as existsSync7, mkdirSync as mkdirSync5, readFileSync as readFileSync11, rmSync as rmSync4, statSync as statSync6, writeFileSync as writeFileSync4 } from "node:fs";
+import { existsSync as existsSync8, mkdirSync as mkdirSync6, readFileSync as readFileSync11, rmSync as rmSync5, statSync as statSync6, writeFileSync as writeFileSync5 } from "node:fs";
 import { homedir as homedir3, hostname as hostname3, userInfo } from "node:os";
 import { dirname as dirname6 } from "node:path";
 import { promisify } from "node:util";
 
 // src/daemon/service.ts
-import { existsSync as existsSync6, statSync as statSync5 } from "node:fs";
-import { delimiter as delimiter2, dirname as dirname5, join as join7, sep as sep3 } from "node:path";
+import { existsSync as existsSync7, statSync as statSync5 } from "node:fs";
+import { delimiter as delimiter2, dirname as dirname5, join as join8, sep as sep4 } from "node:path";
 function defaultServiceManager(platform2 = process.platform) {
   if (platform2 === "darwin") return "launchd";
   if (platform2 === "linux") return "systemd";
@@ -11292,13 +11394,13 @@ function serviceLabel(name2, kind) {
 }
 function unitPath(name2, kind, home) {
   const label = serviceLabel(name2, kind);
-  return kind === "launchd" ? join7(home, "Library", "LaunchAgents", `${label}.plist`) : join7(home, ".config", "systemd", "user", `${label}.service`);
+  return kind === "launchd" ? join8(home, "Library", "LaunchAgents", `${label}.plist`) : join8(home, ".config", "systemd", "user", `${label}.service`);
 }
 function serviceLogPath(configDir, name2) {
-  return join7(configDir, "logs", `runner-${name2}.log`);
+  return join8(configDir, "logs", `runner-${name2}.log`);
 }
 function managedBinary(prefix) {
-  return join7(prefix, "node_modules", ".bin", "tines");
+  return join8(prefix, "node_modules", ".bin", "tines");
 }
 function daemonArgs(input2) {
   const args = [
@@ -11327,7 +11429,7 @@ function daemonArgs(input2) {
 function findOnPath(name2, envPath) {
   for (const dir of (envPath ?? "").split(delimiter2)) {
     if (!dir) continue;
-    const candidate = join7(dir, name2);
+    const candidate = join8(dir, name2);
     try {
       if (statSync5(candidate).isFile()) return candidate;
     } catch {
@@ -11459,7 +11561,7 @@ function matchDaemonProcesses(psOutput, query2) {
       else if (w.startsWith("--name=")) name2 = w.slice("--name=".length);
     }
     if ((name2 ?? query2.hostname) !== query2.name) continue;
-    const root = query2.prefix.endsWith(sep3) ? query2.prefix : query2.prefix + sep3;
+    const root = query2.prefix.endsWith(sep4) ? query2.prefix : query2.prefix + sep4;
     matches.push({ pid, args, managed: args.includes(root) });
   }
   return matches;
@@ -11469,7 +11571,7 @@ function daemonStartedLine(name2) {
   return new RegExp(`(reconnecting as runner|registered runner) "${escaped}"`);
 }
 function managedBinaryPresent(prefix) {
-  return existsSync6(managedBinary(prefix));
+  return existsSync7(managedBinary(prefix));
 }
 
 // src/commands/runner-service.ts
@@ -11520,11 +11622,11 @@ async function waitForStart(logPath, offset, name2) {
   const pattern = daemonStartedLine(name2);
   const deadline = Date.now() + STARTUP_TIMEOUT_MS;
   while (Date.now() < deadline) {
-    if (existsSync7(logPath)) {
+    if (existsSync8(logPath)) {
       const content = readFileSync11(logPath, "utf8").slice(offset);
       if (pattern.test(content)) return true;
     }
-    await new Promise((resolve2) => setTimeout(resolve2, 500));
+    await new Promise((resolve3) => setTimeout(resolve3, 500));
   }
   return false;
 }
@@ -11543,7 +11645,7 @@ function registerServiceCommands(runnerCmd) {
     const kind = resolveServiceManager(opts.serviceManager);
     const baseUrl = resolveUrl(opts).replace(/\/+$/, "");
     const configDir = defaultConfigDir();
-    mkdirSync5(configDir, { recursive: true });
+    mkdirSync6(configDir, { recursive: true });
     const prefix = agentCliPrefix(configDir);
     const ps = await listProcesses();
     const running = ps ? matchDaemonProcesses(ps, {
@@ -11622,9 +11724,9 @@ stop it first \u2014 \`tines runners pause ${settings.name}\`, wait for 0 active
       logPath,
       env: process.env.TINES_CONFIG_DIR ? { TINES_CONFIG_DIR: process.env.TINES_CONFIG_DIR } : {}
     };
-    mkdirSync5(dirname6(target.unitPath), { recursive: true });
-    mkdirSync5(dirname6(logPath), { recursive: true });
-    writeFileSync4(target.unitPath, renderUnit(spec), { mode: 420 });
+    mkdirSync6(dirname6(target.unitPath), { recursive: true });
+    mkdirSync6(dirname6(logPath), { recursive: true });
+    writeFileSync5(target.unitPath, renderUnit(spec), { mode: 420 });
     log2(`wrote ${target.unitPath}`);
     const offset = fileSize(logPath);
     await runServiceCommands(serviceCommands(target).load);
@@ -11656,7 +11758,7 @@ stop it first \u2014 \`tines runners pause ${settings.name}\`, wait for 0 active
   ).option("--service-manager <kind>", "launchd | systemd (default: the one this OS ships)").option("--json", "print JSON instead of a message").action(async (name2, opts) => {
     const kind = resolveServiceManager(opts.serviceManager);
     const target = serviceTarget(name2 ?? hostname3(), kind);
-    if (!existsSync7(target.unitPath)) {
+    if (!existsSync8(target.unitPath)) {
       die(
         `"${target.name}" is not installed as a service (no ${target.unitPath}); run \`tines runner install --name ${target.name} \u2026\` first`
       );
@@ -11671,9 +11773,9 @@ stop it first \u2014 \`tines runners pause ${settings.name}\`, wait for 0 active
   ).option("--service-manager <kind>", "launchd | systemd (default: the one this OS ships)").option("--json", "print JSON instead of a message").action(async (name2, opts) => {
     const kind = resolveServiceManager(opts.serviceManager);
     const target = serviceTarget(name2 ?? hostname3(), kind);
-    const existed = existsSync7(target.unitPath);
+    const existed = existsSync8(target.unitPath);
     await runServiceCommands(serviceCommands(target).unload);
-    rmSync4(target.unitPath, { force: true });
+    rmSync5(target.unitPath, { force: true });
     if (opts.json)
       return printJson({ name: target.name, service_manager: kind, removed: existed });
     log2(
@@ -12752,12 +12854,12 @@ function register10(program3) {
     const api = client(opts);
     const overrides = {};
     for (const spec of opts.state) {
-      const sep4 = spec.lastIndexOf("=");
-      if (sep4 < 1 || sep4 === spec.length - 1) {
+      const sep5 = spec.lastIndexOf("=");
+      if (sep5 < 1 || sep5 === spec.length - 1) {
         die(`--state must look like <workflow>/<state>=<n>, got "${spec}"`);
       }
-      const limit = Number.parseInt(spec.slice(sep4 + 1), 10);
-      const { state } = await resolveStateFlag(api, spec.slice(0, sep4));
+      const limit = Number.parseInt(spec.slice(sep5 + 1), 10);
+      const { state } = await resolveStateFlag(api, spec.slice(0, sep5));
       overrides[state.id] = limit;
     }
     const settings = await api.updateSupervisorSettings({
@@ -13262,7 +13364,7 @@ function pinnedLookup(addresses) {
 }
 async function readHop(url, options) {
   const pinned = await pinnedAddresses(url, options.lookup);
-  return new Promise((resolve2, reject) => {
+  return new Promise((resolve3, reject) => {
     const request = (url.protocol === "https:" ? httpsRequest : httpRequest)(
       url,
       {
@@ -13278,7 +13380,7 @@ async function readHop(url, options) {
           const location = response.headers.location;
           if (!location) return reject(new Error("publication redirect has no destination"));
           try {
-            return resolve2({ redirect: new URL(location, url) });
+            return resolve3({ redirect: new URL(location, url) });
           } catch {
             return reject(new Error("publication redirect has an invalid destination"));
           }
@@ -13313,7 +13415,7 @@ async function readHop(url, options) {
         response.on("error", reject);
         response.on("end", () => {
           try {
-            resolve2({
+            resolve3({
               body: new TextDecoder("utf-8", { fatal: true, ignoreBOM: true }).decode(
                 Buffer.concat(chunks)
               )
@@ -13540,9 +13642,9 @@ async function resolveStateBases(states, library) {
   }
 }
 function resolveBasePair(lib, pair, stateName) {
-  const sep4 = pair.indexOf("/");
-  const workflowRef = pair.slice(0, sep4).trim();
-  const stateRef2 = pair.slice(sep4 + 1).trim();
+  const sep5 = pair.indexOf("/");
+  const workflowRef = pair.slice(0, sep5).trim();
+  const stateRef2 = pair.slice(sep5 + 1).trim();
   const where = `state "${stateName}" inherits from "${pair}"`;
   if (!workflowRef || !stateRef2) {
     die(`${where}, which is not a <workflow>/<state> pair`);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "tines",
-  "version": "0.0.277",
+  "version": "0.0.279",
   "description": "CLI for Tines, an orchestration layer for AI agents",
   "repository": {
     "type": "git",